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A transferable double exponential potential for condensed phase simulations of small molecules
The Lennard–Jones potential is the most widely-used function for the description of non-bonded interactions in transferable force fields for the condensed phase. This is not because it has an optimal functional form, but rather it is a legacy resulting from when computational expense was a major con...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
RSC
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10408570/ https://www.ncbi.nlm.nih.gov/pubmed/38013814 http://dx.doi.org/10.1039/d3dd00070b |
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author | Horton, Joshua T. Boothroyd, Simon Behara, Pavan Kumar Mobley, David L. Cole, Daniel J. |
author_facet | Horton, Joshua T. Boothroyd, Simon Behara, Pavan Kumar Mobley, David L. Cole, Daniel J. |
author_sort | Horton, Joshua T. |
collection | PubMed |
description | The Lennard–Jones potential is the most widely-used function for the description of non-bonded interactions in transferable force fields for the condensed phase. This is not because it has an optimal functional form, but rather it is a legacy resulting from when computational expense was a major consideration and this potential was particularly convenient numerically. At present, it persists because the effort that would be required to re-write molecular modelling software and train new force fields has, until now, been prohibitive. Here, we present Smirnoff-plugins as a flexible framework to extend the Open Force Field software stack to allow custom force field functional forms. We deploy Smirnoff-plugins with the automated Open Force Field infrastructure to train a transferable, small molecule force field based on the recently-proposed double exponential functional form, on over 1000 experimental condensed phase properties. Extensive testing of the resulting force field shows improvements in transfer free energies, with acceptable conformational energetics, run times and convergence properties compared to state-of-the-art Lennard–Jones based force fields. |
format | Online Article Text |
id | pubmed-10408570 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | RSC |
record_format | MEDLINE/PubMed |
spelling | pubmed-104085702023-08-09 A transferable double exponential potential for condensed phase simulations of small molecules Horton, Joshua T. Boothroyd, Simon Behara, Pavan Kumar Mobley, David L. Cole, Daniel J. Digit Discov Chemistry The Lennard–Jones potential is the most widely-used function for the description of non-bonded interactions in transferable force fields for the condensed phase. This is not because it has an optimal functional form, but rather it is a legacy resulting from when computational expense was a major consideration and this potential was particularly convenient numerically. At present, it persists because the effort that would be required to re-write molecular modelling software and train new force fields has, until now, been prohibitive. Here, we present Smirnoff-plugins as a flexible framework to extend the Open Force Field software stack to allow custom force field functional forms. We deploy Smirnoff-plugins with the automated Open Force Field infrastructure to train a transferable, small molecule force field based on the recently-proposed double exponential functional form, on over 1000 experimental condensed phase properties. Extensive testing of the resulting force field shows improvements in transfer free energies, with acceptable conformational energetics, run times and convergence properties compared to state-of-the-art Lennard–Jones based force fields. RSC 2023-07-10 /pmc/articles/PMC10408570/ /pubmed/38013814 http://dx.doi.org/10.1039/d3dd00070b Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by/3.0/ |
spellingShingle | Chemistry Horton, Joshua T. Boothroyd, Simon Behara, Pavan Kumar Mobley, David L. Cole, Daniel J. A transferable double exponential potential for condensed phase simulations of small molecules |
title | A transferable double exponential potential for condensed phase simulations of small molecules |
title_full | A transferable double exponential potential for condensed phase simulations of small molecules |
title_fullStr | A transferable double exponential potential for condensed phase simulations of small molecules |
title_full_unstemmed | A transferable double exponential potential for condensed phase simulations of small molecules |
title_short | A transferable double exponential potential for condensed phase simulations of small molecules |
title_sort | transferable double exponential potential for condensed phase simulations of small molecules |
topic | Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10408570/ https://www.ncbi.nlm.nih.gov/pubmed/38013814 http://dx.doi.org/10.1039/d3dd00070b |
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